DNA Overview: how THIRD Generation Sequencing is revolutionising Kennedy DNA testing! (May 2019 update)

Promotional video still of the 10X Genomics Linked Reads system

05.05.2019 update.

This page covers phases 2 and 3 of my Kennedy DNA study, historical notes on phase 1 and some haplogroup notes about my own Y chromosome group (M222, FGC4077 and FGC5856), and finally some remarks on the ever popular autosomal tests.

Kennedy DNA study Phase 3 (2019+)

Phase 3 of the project is examining third generation long read sequencing technologies from Oxford Nanopore and PacBio, along with the 10X Genomics Chromium Linked Read system which adds barcoding to traditional second generation sequencing. As of May 2019 these tests are all available for exploration but are still on the expensive side and their benefits in genetic ancestry and surname studies are still to be established. So far the only one I have personal results for is the 10X Genomics Chromium system. Some early comments can be found in my sequencing summary report but the bulk of the output has still to be analysed.

Kennedy DNA study Phase 2 (2013-2019+)

The seeds for phase 2 were probably sown in 2012 with the publication of the citizen science paper by Rocca et al. on mass SNP discovery and Dr. J Wilson's sequencing of two R-M222 males, resulting in the breakthrough 2013 SNP array test called 'Chromo2'. This affordable test for the first time enabled surname projects to switch over to a SNP-first approach. Chromo2 was rapidly overtaken by more flexible SNP test panels developed by Dr. T. Krahn, one of Rocca's co-authors, made available via his 'YSEQ' lab in Berlin. The advantage of the SNP/next-generation sequencing method is simply that the rates of false positives are virtually zero - in fact since 2013 there has not been a single false positive in the Kennedy project. Professor Mark Jobling* (2017) writes "SNPs define stable haplotypes, known as haplogroups, which can be used to build a robust phylogeny using the principle of maximum parsimony". Depending on budget and whether funding is coming from the project, testing usually involves the YSEQ lab for single and fixed panel SNP testing and either YSEQ or Full Genomes Inc. for the more advanced sequencing (sometimes loosely referred to as 'SNP discovery' testing).

Further background on the explosive growth in Y-SNPs can be found in the article 'The Y-Chromosome Tree Bursts into Life'; this was published in December 2014 since which time the tree has grown in size by a further entire order of magnitude.

Most of the branches studied during Phase 1 have now been retested using SNP testing methods, as well as using the latter for new samples. With SNP results it is much easier to draw unambiguous 'trees' (cladograms) showing the exact relationships of all the Kennedy branches. The R-M222 part of the overall Kennedy results tree is public on this site and shares results with general M222 men due to surname-haplogroup collaboration efforts (see the M222 secton below). Men sequenced by the project who lie outside M222 can be seen on the YFull Y chromosome tree. All the Scottish and Ulster branch discoveries were made by my project. Dr. Thomas Krahn identified the core marker for the Tipperary ('Dalcassian') O'Kennedys in 2009.

The project will cover the costs of testing if a male Kennedy is available with a proven paper trail to a rural parish in Scotland or Ireland. Men not qualifying under those conditions are of course more than welcome to test under direction of the project. As of October 2018 funding may be extended to cover the more detailed sequencing test on a 'while stocks last' basis. This free test is worth over 600 Euros. There are currently 19 kits sequenced or being sequenced as of mid March 2019! A choice of European or American lab is available.


Kennedy DNA study Phase 1 (2004-2012)

The depracated Y-STR testing method was commercialized back in 2000, using techniques explored by academics Dr. Bryan Sykes and Dr. Mark Thomas. Their papers on the Sykes surname and the Cohanim priesthood set the scene for what ultimately turned out to be a flawed matching system which in some instances could have 'false positive' rates exceeding 90%. My own Y-STR testing commenced in 2004 and from 2006 to early 2013 I tested considerable numbers of male Kennedys using this method. This data now has to be considered obsolete.

The M222, FGC4077 and FGC5856 haplogroups (2006-2019+)

I was a first day tester of the M222 SNP in early 2006 when Drs. James Wilson and David Faux first put it on sale at the sadly missed Ethnoancestry lab. Because of this I divide my time between the Kennedy surname project and M222 research - of course my interest grows as I near my own sub-branch M222-FGC4077 and then FGC5856. Kennedys occur in no less than EIGHT sub-branches of M222. This is why I publish a joint chart of M222 and Kennedy data. This tree extends upwards and sideways but the non-M222 sections are not online at the time of writing. The chart is on pdf format and can be text searched for surnames of interest eg Kennedy!

So what exactly is this chart? Originally it was designed as a CHROMO2 RESULTS TRACKER. Therefore the tree it started off with was of course the Dr. Wilson M222 tree published during the rollout of Chromo2. Within weeks my own sequencing data had determined that FGC4077 was the branch accounting for most of the unassigned testers on Chromo2 and so this branch was added to the tree. As I identified new branches these and the test surnames were also added. At all times branches were only added after I had proven them to my satisfaction based on raw data. Apart from the original Wilson markers (which numbered around 24) it was my own work and not copied from anyone else's tree. This research continued until mid-2015 when I reduced my direct work and started to rely more on the analysis work of YFull.com who do professional BAM data analysis. I co-admin the YFull M222 project with Aidan Byrne. A review of the history of M222 research from 1999 onwards can be read here.

Following my own sequencing and the discovery that the FGC4077 branch represented in excess of 10% of all M222 men, informal group discussions led to a suggestion to create a mailing list which was set up by Gerry Hoy, I act as the admin/moderator. Results are shared via my M222 chart and the YFull R-Y3454 tree their name for the group). This group covers everything at or below FGC4077, FGC4078, FGC4087, A725, FGC12948, FGC5856 and A361 sub-branches and so on below. If you have a positive result for one of these, please contact me to join the group.

The M222 SNP chart including the M222 Kennedys is here.

I almost forgot - what about Autosomal testing?!

In the last few years affordable tests from Ancestry.com and 23andMe have become household names and have taken over the bulk of the market share. Both have multi-million sized databases with Ancestry recently announcing they had tested 10+ million men and women (now shipped out 14 million kits!). Most of the markers they test are on the autosomes chromosomes 1 to 22 and the X chromosome. Confusingly though, they do have a small selection of Y chromosome markers as well as mitochondrial (mtDNA) markers. Although they have improved they are not comparable with the detailed and very current Y SNP test panels from YSEQ. The tests are hence good for finding close cousins on all tree branches but poor for deep examination of male kindreds. I continue to urge takers of these two tests to get their raw data uploaded to the comparison site GEDMatch (or Genesis-GEDMatch for the latest 23andMe v5 test). The old GEDMatch data has now been migrated to the Genesis version of the site. If you are a Kennedy, drop me a line with your GEDMatch kit number. We can then discuss whether the raw data contains any Y SNP markers of use. I have done both the Ancestry and 23andMe tests as well as the new LivingDNA test from England. The latter is similar to the first two but the matching database has yet to launch.

* Professor Mark Jobling is a leading UK geneticist and was the Y-SNP consultant to LivingDNA on their new SNP array test.

For further information please contact the project.